SMITHTOWN, Long Island (PIX11) - An FBI investigation is not only probing more deeply into claims that the chief of one of the country’s largest police departments beat up a defenseless suspect, but it may be moving closer to answering unresolved questions that could show that the chief committed further, worse crimes than those of which he’s currently accused.

Suffolk County Police Chief James Burke denies that he physically abused car break-in suspect Chris Loeb, 26, in Loeb’s home and at a local police precinct early in the morning of December 14, 2012. However, Loeb’s mother, who had been at her home when Burke and other officers showed up around 12:30 that morning, responded to news that the case is changing.

“I’m glad for the way things are going,” said Jane Loeb about her son’s situation, “and it’s for the better this way.” She was talking about how the involvement of federal investigators has altered the thrust of the criminal inquiry.

Chris Loeb has been moved from the Suffolk County Jail to a federal lockup in Brooklyn, and he’s expected to testify against Chief Burke as part of a federal grand jury’s probe into allegations that the chief violated Loeb’s civil rights.

Twelve SCPD officers have received federal subpoenas as well. They were present when Chief Burke showed up at Loeb’s home on December 14th, or were on hand after the suspect had been taken to the Fourth Police Precinct later that morning, or both.

At the police facility, Loeb alleges and police sources say, Chief Burke ordered everyone who had been in a room with the criminal suspect to clear out and leave the two of them alone. Loeb has told his family that the chief then beat him severely.

Noting these allegations, people familiar with the case point out that it is very important that the suspect has been moved into federal custody. “That’s good as a safety issue, if this case continues to go where it’s going,” said retired NYPD detective supervisor and PIX11 News commentator Wally Zeins.

Where the case appears to be going puts the investigative spotlight even more intensely on the chief and on details of the interactions between Burke and Loeb last December. Loeb allegedly stole a duffel bag from the chief’s vehicle, as well as other items from about a dozen other cars in Chief Burke’s neighborhood in the village of St. James, as a way for Loeb to make money to support his longstanding drug addiction.

In the duffel bag were the chief’s gun belt, ammunition, handcuffs, and what police describe as “other items” that have yet to be identified. The federal probe could ultimately result in a full inventory of the contents of the chief’s luggage.

“This type of investigation,” former detective Zeins told PIX11 News, “with what they’re putting into it, there’s a lot more to the investigation that we don’t know.”

Other aspects of the case that were put in place long before federal prosecutors became involved also mark the situation as unusual. Even though Loeb had been charged with 29 low-level felony counts, he was given a noticeably high bond of $500,000. Also, a special prosecutor was appointed to his case shortly after Loeb’s arrest.